The HIV-1 reverse transcriptase (RT) heterodimer contains a peptide sequence which was predicted to be a potential leucine zipper, stabilizing subunit association of the p51.p66 heterodimer. Molecular dynamics simulations of 100 ps duration in water at 300 K were performed on the RT peptide and on a portion of GCN4, a transcription control protein which is known to form parallel alpha-helical dimers, in both parallel and anti-parallel orientations. While estimates of the free energy (based on buried hydrophobic surface area) strongly favored the parallel orientation of GCN4, the RT results were ambiguous. Recent publication of a low resolution crystal structure of the HIV RT indicates the peptide is not involve in a leucine zipper. The lack of orientational preference for dimerization of the RT peptide may be indicative of the fact that is does not dimerize at all, in retrospect. A simulation studying the effects of solvation on one of the identical subunits of the dimeric HIV-1 protease was reported previously. The results indicate the anti-parallel beta sheet which acts as a flap covering the enzyme's active site moves as an independent rigid motif, retaining its structure. The N- and C- termini, in contrast, undergo numerous conformational changes. The hydrophobic core also exhibits some relaxation of its tertiary structure, more than is seen in a comparable simulation of the complete dimer or typical globular proteins such as myoglobin. Overall, the structure of solvated monomer is similar, but not identical, to the crystal structure of the dimer; this should be taken into account in efforts to develop drugs designed to interfere with protease dimer formation.